/BIOL6304

Principles of Phylogenetics Texas Tech University

Primary LanguageTeXGNU General Public License v3.0GPL-3.0

BIOL 6304

PRINCIPLES AND PRACTICE OF PHYLOGENETICS

Fall 2022 • TuTh 3:30 - 4:50 PM

Tuesdays - Sciences 204

Thursdays - Biology 405 (Computer Lab)

Instructor: Dr. Matthew Johnson, matt.johnson@ttu.edu, 806-834-5750

Office Hours by Appointment

Textbook: Tree Thinking by Baum and Smith

Website: github.com/mossmatters/BIOL6304

Readings and Thursday exercises will be posted on Blackboard.

Expected Learning Outcomes

After completion of this graduate level course, students will be able to:

  • Correctly use phylogenetic trees to interpret patterns of common descent and trait evolution.
  • Describe the relationship between phylogeny and modern systematics.
  • Reconstruct phylogenetic trees from morphological and molecular data.
  • Evaluate and compare methods for inferring phylogenetic trees and support values.
  • Design and implement a project that uses phylogenetics to solve a relevant question in systematics, ecology, microbiology, or genomics.

Schedule

Tuesday Lecture Topic Reading Thursday Practical Topic
Introduction Tree Thinking Chapters 1 & 2 8/25
8/30 Tree Thinking Tree Thinking Chapter 3 9/1 Interpreting Phylogenies
9/6 Homology Tree Thinking Chapters 4 & 5 9/8 Caminalcules
9/13 Inferring Phylogenies Tree Thinking Chapter 7 9/15 Parsimony
9/20 Molecular Evolution Tree Thinking Chapter 8 (to page 247) 9/22 Molecular Evolution
9/27 Maximum Likelihood Tree Thinking Chapter 9 9/29 Alignment and Tree Inference
10/4 Bayesian Inference Tree Thinking Chapter 8 (from page 247) 10/6 Mr. Bayes
10/11 Gene Trees and Species Trees Tree Thinking Chapter 6 10/13 ASTRAL
10/18 Trait Evolution Tree Thinking Chapter 10 10/20 Ancestral State Reconstruction
10/25 Diversification & Dating Tree Thinking Chapter 11 10/27 Trees in Time and Space
11/1 Community Phylogenetics 11/3 Trees in R Part I
11/8 NO CLASS: ELECTION DAY 11/10 Trees in R Part II
11/15 Phylogenetic Comparative Methods 11/17 Trees in R Part III
11/22 NO CLASS: THANKSGIVING BREAK
11/29 Phylogenomics 12/1 Project Help Session
12/6 Presentations

Methods of Assessing Expected Learning Outcomes

Student learning outcomes will be assessed via:

  • Participation in discussion during Tuesday lectures and Thursday practical exercises.
  • A short written paper early in the semester, in which students demonstrate understanding of tree thinking concepts.
  • A written project proposal designed by the student that implements methods learned in class.
  • A ten-minute pre-recorded presentation showing the results of the proposed project.
  • A 8-10 page project paper.

Evaluation

Particpation. Each week, on Tuesdays there will be lecture material related to required reading indicated in the schedule above. Students are expected to have done the reading before class and to ask questions during lecture. Some weeks there may also be additional group discussion, and participation is encouraged. On Thursdays, students will be given an in-class assignment "practical" to reinforce the topic that week. These assignments will not be graded, but participation is required.

Short Paper. During the first few weeks of class, students will be given an in-class assignment to score "traits" on the Caminalcules, a set of imagined cartoon organisms. Students will be expected to reconstruct a phylogeny from these traits and evaluate support for relationships as if they are preparing a taxonomic monograph of the Caminalcules. The results of this analysis should be written up into a 3-5 page paper describing the methods used to score traits, infer the phylogeny, and taxonomic conclusions. The short paper will be evaluated for correct use of tree thinking. The short paper will be due September 29.

Project Proposal. The main assessment for the course is a small independent project designed and carried out by the student. This project may cover any topic relevant to phylogenetics that is of interest to the student. The project can take many forms, including phylogenetic systematics, comparison of phylogenetic methods, re-analysis of published data, or any type of applied phylogenetics such as community ecology or phylogenomics. Use of data relevant to the student's research project is highly encouraged, but not required. The student may obtain data from the instructor if desired. To ensure the project is appropriate for the class and time frame, a brief proposal for the project (fewer than 500 words) is due October 29.

Project Presentation. On the last day of class (December 6), students will describe the results of their project in a short (8-10 minute) pre-recorded presentation to the class and will upload to Blackboard. Students will be assigned two peer reviewers who will provide feedback according to a presentation rubric. Students will be assessed on clarity of presentation, use of appropriate tree-thinking terminology and phylogenetic methods. The quality of presentation feedback will also be part of the Project Presentation Grade.

Project Paper. Students will prepare a 8-10 page (double-spaced) report describing their project. The report should take the form of a peer-reviewed scientific paper, with an introduction, materials and methods, results and discussion, and references. Project papers must include at least two figures and/or tables, which will not be considered part of the overall paper length. Students may choose any format for citations and references (i.e. footnotes or in-line citations) but must remain internally consistent. Project papers will be evaluated for providing appropriate context for the project in the phylogenetic literature, correct application of tree thinking, the phylogenetic methods, and the logic of the conclusions drawn. Students will not be evaluated on whether their project "worked," as experimentation is encouraged. A full grading rubric will be supplied to students later in the semester. The final paper is due one week after the presentations, on December 13.

Grading Policy

  • Participation: 30%
  • Short Paper: 10%
  • Project Proposal: 15%
  • Project Presentation: 15%
  • Project Paper: 30%

Letter Grades: A = 100-90; B = 89.9-80; C = 79.9-70; D = 69.9-60; F = < 59.9.

All grades posted at the end of the course will be final, except for calculation errors!

Course Policies and Resources

COVID Contingency Statement

This course is being taught primarily in the face-to-face learning mode. The University will continue to monitor CDC, State, and TTU System guidelines in continuing to manage the campus implications of COVID-19. Any changes affecting class policies or delivery modality will be in accordance with those guidelines and announced as soon as possible. If Texas Tech University campus operations are required to change because of health concerns related to the COVID-19 pandemic, it is possible that this course will move to a fully online delivery format. Should that be necessary, students will need to have access to the Internet, a webcam, and microphone for remote delivery of the class.

Although COVID-19 vaccinations are not mandated, Texas Tech strongly recommends that all students be vaccinated and receive a booster when eligible. The vaccines are safe and effective. Please visit the university’s coronavirus (COVID-19) page for additional information about on-campus vaccination and testing schedules, reporting a positive test result, and submitting vaccination records.

Face masks are strongly encouraged in classrooms and other public indoor settings on campus, including the Student Wellness Center.

Self-isolation for five days is required for all students (vaccinated or unvaccinated) who test positive for COVID-19. After the five-day isolation period, if the student is asymptomatic or their symptoms are resolving (fever free without the use of fever reducing medication for 24 hours), they may return to class/activities but should wear a face mask for an additional five days.

Students who are positive should report the result. This generates a letter that you can provide to your professors and instructors, notifying them of your positive diagnosis.

Illness-Based Absence Policy

If at any time during this semester you feel ill, in the interest of your own health and safety as well as the health and safety of your instructors and classmates, you are encouraged not to attend face-to-face class meetings or events. If you suspect the illness is related to COVID19, please follow the procedure above and report any positive test result.

For all other illnesses, please do not come to class if you are sick. I am happy to work with any student to cover any missed material and extend deadlines as needed. Mental health is health. If you are having difficulties that prevent you from participating in class, please let me know and I will be happy to work with you to complete your learning objectives.

If your illness prevents you from attending class or submitting assignments for more than two weeks, you should contact the Dean of Students.

Civility in the Classroom

You are expected to conduct yourselves in such a way as to provide a good learning environment for yourself and other students. Therefore, disruptions or behaviors that affect your ability to learn and that of other students will not be tolerated. If you are being disruptive, you will be asked to leave.

During in-class discussions, please be respectful of each other's time and the time of the instructor. Language that is hostile or discriminatory will not be tolerated. Be mindful of microagressions; be aware that your actions can be hurtful to others and contribute to a negative environment even if you had no intent of harm. Work towards an inclusive environment in the classroom.

Academic Honesty

It is the aim of the faculty of Texas Tech University to foster a spirit of complete honesty and high standard of integrity. The attempt of students to present as their own any work not honestly performed is regarded by the faculty and administration as a most serious offense and renders the offenders liable to serious consequences, possibly suspension. "Scholastic Dishonesty" includes, but is not limited to, cheating, plagiarism, collusion, falsifying academic records, misrepresenting facts, and any act designed to give unfair academic advantage to the student (such as, but not limited to, submission of essentially the same written assignment for two courses without the prior permission of the instructor) or the attempt to commit such an act.

Plagiarism on projects and presentations will not be tolerated. I will be using resources including turnitin.net to evaluate student papers for evidence of plagiarism. In academic communication, plagiarism is not limited to simply copying another's work, but may also include improper citation of facts, results, and quotations. If you are unsure, please ask me prior to turning in the assignment. Once an assignment is turned in, I will not tolerate any form of plagiarism. Any form of plagiarism will be met with a "0" for that assignment, and violations will be referred to the Office of Student Conduct to determine appropriate disciplinary action.

WITHDRAWAL/DROPPING THE CLASS (TTU OP 34.05)

Students may officially drop a course through the 45th class day of a long semester or the 15th class day of a summer term and receive the grade of W regardless of their progress in the class. Students must determine the deadline for dropping this semester. After the deadline, the student must complete the course for a grade.

INCOMPLETE (TTU OP 34.12, 34.05)

Grades of I may be applicable when circumstances beyond the student's control, such as illness or impairment due to an accident, prevent the student from completing course requirements. The instructor assigning the grade will stipulate in writing at the time the grade is given the conditions under which the I may be removed. The assigned work and a change of grade must be recorded within one calendar year from the date of the I. Failure to do so results in an F for that course.

ADA STATEMENT (OP 34.22):

Any student who, because of a disability, may require special arrangements in order to meet the course requirements should contact the instructor as soon as possible to make any necessary arrangements. Students should present appropriate verification from Student Disability Services during the instructor's office hours. Please note: instructors are not allowed to provide classroom accommodations to a student until appropriate verification from Student Disability Services has been provided. For additional information, please contact Student Disability Services in West Hall or call 806.742.2405.

RELIGIOUS HOLY DAYS

"Religious holy day" means a holy day observed by a religion whose places of worship are exempt from property taxation under Texas Tax Code.

  • A student who intends to observe a religious holy day should make that intention known in writing to the instructor prior to the absence.
  • A student who is absent from classes for the observance of a religious holy day shall be allowed to take an examination or complete an assignment scheduled for that day within a reasonable time after the absence.
  • A student who is excused under section 2 may not be penalized for the absence; however, the instructor may respond appropriately if the student fails to complete the assignment satisfactorily.

LQBTQIA

I identify as an ally to the lesbian, gay, bisexual, transgender, queer, intersex, and asexual (LGBTQIA) community, and I am available to listen and support you in an affirming manner. I can assist in connecting you with resources on campus to address problems you may face pertaining to sexual orientation and/or gender identity that could interfere with your success at Texas Tech. Additional resources are available through the Office of LGBTQIA within the Center for Campus Life, Student Union Building Room 201, 806.742.5433.

TTU Resources for Discrimination, Harassment, and Sexual Violence

Texas Tech University is committed to providing and strengthening an educational, working, and living environment where students, faculty, staff, and visitors are free from gender and/or sex discrimination of any kind. Sexual assault, discrimination, harassment, and other Title IX violations are not tolerated by the University. Report any incidents to the Office for Student Rights & Resolution, 806-742-SAFE (7233) or file a report online at http://titleix.ttu.edu/students. Faculty and staff members at TTU are committed to connecting you to resources on campus. Some of these available resources are: